Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate 16354 b2247 predicted enolase (RefSeq)
Query= BRENDA::G3YE52 (383 letters) >FitnessBrowser__Keio:16354 Length = 401 Score = 89.0 bits (219), Expect = 2e-22 Identities = 87/279 (31%), Positives = 134/279 (48%), Gaps = 31/279 (11%) Query: 17 LFVKIVDEDGQCGWGESTL-EGHTEAVEGTLNALCKRFQGYEADDIEHIW-QMAWRLGFY 74 L V++ E+GQ G+ ST E VE LN +G DI+ I QM +Y Sbjct: 66 LVVEVEAENGQTGFAVSTAGEMGCFIVEKHLNRF---IEGKCVSDIKLIHDQMLSATLYY 122 Query: 75 RG-GPVFMSAISGIDIALWDLKGRRLGVPIYQLLGGKVRNKLSVYAWIGGDRPSDVEAAG 133 G G + M+ IS +D+ALWDL G+ +G+P+Y+LLGG VR+++ YA G RP + Sbjct: 123 SGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYA--TGARPDLAK--- 177 Query: 134 KARLAQGFKAIKMNATEDINWLDSPRALDSSVERLKTVKA-----LGLD--AALDFHGRL 186 GF KM +W P D+ + + + A G D LD Sbjct: 178 ----EMGFIGGKM----PTHW--GPHDGDAGIRKDAAMVADMREKCGEDFWLMLDCWMSQ 227 Query: 187 HKPMAKQLAKALEPHRPLFLEEPLLSEHPEAIKQL--SDQVSCPIALGERLYSRWDVKRF 244 A +LA A P+ ++EE L + E+ ++L + V + GE + R Sbjct: 228 DVNYATKLAHACAPYNLKWIEECLPPQQYESYRELKRNAPVGMMVTSGEH-HGTLQSFRT 286 Query: 245 LEDASVDILQPDIAHCGGISELRRIASMAETYDVAIAPH 283 L + +DI+QPD+ CGG++ L IA++A++ + PH Sbjct: 287 LSETGIDIMQPDVGWCGGLTTLVEIAAIAKSRGQLVVPH 325 Lambda K H 0.320 0.138 0.429 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 385 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 401 Length adjustment: 31 Effective length of query: 352 Effective length of database: 370 Effective search space: 130240 Effective search space used: 130240 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory